Equilibrium Association Research Articles

Effect of substitution of methanatoboron difluoride derivatives on non-covalent interactions with tetraphenylporphyrin

Tetraphenylporphyrin (TPP) forms non-covalent supra-molecular complexes with methanatoboron difluoride (MBDF) derivatives in dichloromethane. The photo-chemical properties of the association equilibrium of free TPP and MBDFs with the respective supra-molecular complexes were investigated in the ground state. There is formation of isosbestic points which had been taken as proof of the existence of equilibrium between the absorbing species. Monte Carlo simulation and Density functional theory calculation established the experimental results of non-covalent interactions in terms of loss of planarity and frontier molecular orbital calculations defines the electron donor and acceptor. The direction of electron flow is confirmed by the electrochemical indices. The electron rich substituent in MBDF favours the non-covalent binding ability between TPP and MBDF. Both H-bonding and charge transfer interactions are primarily responsible in stabilising these complexes.
 Bangladesh J. Sci. Ind. Res. 57(3), 163-172, 2022

Real-time kinetics and affinity analysis of the interaction between protein A and immunoglobulins G derived from different species on silica colloidal crystal films

Kinetic and affinity analysis of protein interactions reveals information on their related activities in biological processes. Herein, we established a system for evaluating the kinetics and affinity of the interaction between protein A and various IgG species on the surface of silica spheres of silica colloidal crystal (SCC) films by the extraordinary optical interference capabilities of 190 nm silica spheres after self-assembly. The equilibrium association constant (KA) was calculated by the equilibrium Langmuir model and nonlinear least-squares analysis of time-dependent data. The relative protein A/IgG binding affinity is human > rabbit >cow >goat. In addition, the competitive interaction of distinct species of IgG with protein A at the interface of SCC films was studied and performed. These findings may help with the use of protein A and other recognition components in a number of sensor types. Furthermore, this research might offer a novel approach to determining the kinetics and affinity of proteins on the surface of spheres particles, which may contribute to the development of the application of spheres particles in pharmaceutical science, biomedical engineering, and other techniques.

Sulfate Protonation in Sodium Chloride and Sodium Perchlorate Media

The equilibrium (association) constant, KA, for the first protonation of the sulfate ion in aqueous solution: [H+(aq) + {text{SO}}_{4}^{2 - }(aq) ⇌ {text{HSO}}_{4}^{ - }(aq)] has been measured at 298.15 K in NaCl and NaClO4 media using glass-electrode potentiometry at five ionic strengths in the range 0.5 ≤ I/(mol·dm−3) ≤ 5.0. The present KA values vary smoothly with I and are in good agreement with reliable literature data but indicate that the previously reported value of KA at I = 5 mol·dm−3 in NaClO4 media is in error.

Determination of association equilibrium constant from single molecule fluorescence localization microscopy.

Single molecule fluorescence localization microscopy provides molecular localization with a precision in the tens of nanometer range in the plane perpendicular to the light propagation. This opens the possibility to count molecules and correlate their locations, starting from a map of the actual positions in a single molecule super resolution image. Considering molecular pair correlation as an indication of interaction, and a way to discern them from free molecules, we describe a method to calculate thermodynamic equilibrium constants. In this work, we use as a test system two complementary homo-oligonucleotides, one strand marked with Cyanine 3.5 and the other with Alexa Fluor 647. Hybridization is controlled by the amount of each strand, temperature, and the ionic force, and measured in steady state emission. The same samples are examined in Stochastic Optical Reconstruction Microscopy (STORM) experiments with split-field simultaneous two-colour detection. The effect of multiblinking, labelling-detection efficiency, and determination of the critical distance for association are discussed. We consistently determine values in STORM coincident with those of the bulk experiment.

Investigation and Comparison of Specific Antibodies' Affinity Interaction with SARS-CoV-2 Wild-Type, B.1.1.7, and B.1.351 Spike Protein by Total Internal Reflection Ellipsometry.

SARS-CoV-2 vaccines provide strong protection against COVID-19. However, the emergence of SARS-CoV-2 variants has raised concerns about the efficacy of vaccines. In this study, we investigated the interactions of specific polyclonal human antibodies (pAb-SCoV2-S) produced after vaccination with the Vaxzevria vaccine with the spike proteins of three SARS-CoV-2 variants of concern: wild-type, B.1.1.7, and B.1.351. Highly sensitive, label-free, and real-time monitoring of these interactions was accomplished using the total internal reflection ellipsometry method. Thermodynamic parameters such as association and dissociation rate constants, the stable immune complex formation rate constant (kr), the equilibrium association and dissociation (KD) constants and steric factors (Ps) were calculated using a two-step irreversible binding mathematical model. The results obtained show that the KD values for the specific antibody interactions with all three types of spike protein are in the same nanomolar range. The KD values for B.1.1.7 and B.1.351 suggest that the antibody produced after vaccination can successfully protect the population from the alpha (B.1.1.7) and beta (B.1.351) SARS-CoV-2 mutations. The steric factors (Ps) obtained for all three types of spike proteins showed a 100-fold lower requirement for the formation of an immune complex when compared with nucleocapsid protein.

On Computing Equilibrium Binding Constants for Protein-Protein Association in Membranes.

Protein association in lipid membranes is fundamental to membrane protein function and of great biomedical relevance. All-atom and coarse-grained models have been extensively used to understand the protein-protein interactions in the membrane and to compute equilibrium association constants. However, slow translational and rotational diffusion of protein in membrane presents challenges to the effective sampling of conformations defining the ensembles of free and bound states contributing to the association equilibrium and the free energy of dimerization. We revisit the homodimerization equilibrium of the TM region of glycophorin A. Conformational sampling is performed using umbrella sampling along previously proposed one-dimensional collective variables and compared with sampling over a two-dimensional collective variable space using the MARTINI v2.2 force field. We demonstrate that the one-dimensional collective variables suffer from restricted sampling of the native homodimer conformations leading to a biased free energy landscape. Conversely, simulations along the two-dimensional collective variable effectively characterize the thermodynamically relevant native and non-native interactions contributing to the association equilibrium. These results demonstrate the challenges associated with accurately characterizing binding equilibria when multiple poses contribute to the bound state ensemble.

Interaction of methylene blue with SDS in the premicellar solution of CPC in the aqueous and methanol-water system

Interactions between sodium dodecyl sulfate (SDS) and methylene blue (MB) have been studied in presence of cetylpyridinium chloride (CPC) in aqueous and methanol-water binary solvents via conductometric and tensiometric methods. The experiment was conducted to see the possibility of a synergistic effect of the SDS+CPC system and changes in the interactional behavior of SDS with MB in presence of CPC. The value of the molecular interaction parameter for micellization (βM) was found to be negative from the experimental results and the value of |βM| was found to be greater than ln(CMCSDS / CMCCPC), which didn’t describe synergism completely but indicated the strong striking interactions between the oppositely charged surfactants. However, the CMC of the SDS+CPC system was found to be very low as compared to the CMC of SDS alone. This result of CMC based on striking interactions between oppositely charged surfactants was used to calculate various parameters like Gibb’s free energy of micellization (∆Gmo), surface excess(Γmax), minimum surface area (Amin), surface pressure πCMC, standard free energy of adsorption (∆Gadso), pC20, minimum surface free energy (Gmins), packing parameter (P) and association equilibrium constant (K). The addition of methanol as a cosolvent enhances the CMC and α value of the SDS+CPC as well as the SDS+CPC-MB system. Correlation of ∆Gmo with different solvent parameters namely Gordon parameter (G), Reichardt's parameter (ET (30)), viscosity (ηo), and solvophobic parameter (SP) has also been evaluated.

Nanopore-Based Single-Entity Electrochemistry for the Label-Free Monitoring of Single-Molecule Glycoprotein-Boronate Affinity Interaction and Its Sensing Application.

Nanopipettes provide a promising confined space that enables advances in single-molecule analysis, and their unique conical tubular structure is also suitable for single-cell analysis. In this work, functionalized-nanopore-based single-entity electrochemistry (SEE) analysis tools were developed for the label-free monitoring of single-molecule glycoprotein-boronate affinity interaction for the first time, and immunoglobulin G (IgG, one of the important biomarkers for many diseases such as COVID-19 and cancers) was employed as the model glycoprotein. The principle of this method is based on a single glycoprotein molecule passing through 4-mercaptophenylboronic acid (4-MPBA)-modified nanopipettes under a bias voltage and in the meantime interacting with the boronate group from modified 4-MPBA. This translocation and affinity interaction process can generate distinguishable current blockade signals. Based on the statistical analysis of these signals, the equilibrium association constant (κa) of single-molecule glycoprotein-boronate affinity interaction was obtained. The results show that the κa of IgG in the confined nanopore at the single-molecule level is much larger than that measured in the open system at the ensemble level, which is possibly due to the enhanced multivalent synergistic binding in the restricted space. Moreover, the functionalized-nanopore-based SEE analysis tools were further applied for the label-free detection of IgG, and the results indicate that our method has potential application value for the detection of glycoproteins in real samples, which also paves way for the single-cell analysis of glycoproteins.

High-throughput biochemical profiling reveals functional adaptation of a bacterial Argonaute

Argonautes are nucleic acid-guided proteins that perform numerous cellular functions across all domains of life. Little is known about how distinct evolutionary pressures have shaped each Argonaute's biophysical properties. We applied high-throughput biochemistry to characterize how Thermus thermophilus Argonaute (TtAgo), a DNA-guided DNA endonuclease, finds, binds, and cleaves its targets. We found that TtAgo uses biophysical adaptations similar to those of eukaryotic Argonautes for rapid association but requires more extensive complementarity to achieve high-affinity target binding. Using these data, we constructed models for TtAgo association rates and equilibrium binding affinities that estimate the nucleic acid- and protein-mediated components of the target interaction energies. Finally, we showed that TtAgo cleavage rates vary widely based on the DNA guide, suggesting that only a subset of guides cleaves targets on physiologically relevant timescales.

Van’t Hoff analysis of CLC-ec1 dimerization in Escherichia coli lipid membranes

What are the thermodynamic forces that drive hydrophobic membrane proteins to form stable complexes with other hydrophobic proteins in the greasy lipid solvent? In order to investigate this question, we must have a way of dissecting the changes in thermodynamic properties, i.e. enthalpy and entropy, associated with membrane protein reactions. The CLC-ec1 chloride/proton antiporter forms a homodimer that participates in an association equilibrium with a dimerization free energy of −13 kcal/mole in E.

Statistical predictions on the encapsulation of single molecule binding pairs into sized-dispersed nanocontainers.

Single molecule experiments have recently attracted enormous interest. Many of these studies involve the encapsulation of a single molecule into nanoscale containers (such as vesicles, droplets and nanowells). In such cases, the single molecule encapsulation efficiency is a key parameter to consider in order to get a statistically significant quantitative information. It has been shown that such encapsulation typically follows a Poisson distribution and such theory of encapsulation has only been applied to the encapsulation of single molecules into perfectly sized monodispersed containers. However, experimentally nanocontainers are usually characterized by a size distribution, and often just a single binding pair (rather than a single molecule) is required to be encapsulated. Here the use of Poisson distribution is extended to predict the encapsulation efficiency of two different molecules in an association equilibrium. The Poisson distribution is coupled with a log-normal distribution in order to consider the effect of the container size distribution, and the effect of adsorption to the container is also considered. This theory will allow experimentalists to determine what single molecule encapsulation efficiency can be expected as a function of the experimental conditions. Two case studies, based on experimental data, are given to support the theoretical predictions.

Nexus between exports, imports and foreign direct investment: Evidence from Bangladesh

Foreign Direct Investment (FDI) plays a significant role in international trade (IT). Numerous recent studies focused on the FDI-IT nexus and found a strong interrelation between the two variables. The current research empirically examines the causal linkage among imports, exports, and FDI in Bangladesh, utilizing available time-series data from 1980-2015. The study finds that the long-run equilibrium association exists among Exports, Imports and FDI. The study also finds unidirectional causality running from imports and exports to FDI, meaning the rise and fall of exports and imports cause an increase or decrease in FDI of Bangladesh, respectively, and there is no other long-run causality found among other variables. In the short run, unilateral causality is running from imports to FDI, imports to export and exports to FDI. These empirical findings mean that expanding trade can be used to attract more FDI in Bangladesh. Therefore, the study findings strongly support the notion that international trade (exports and imports) stem from the attraction of FDI. IIUC Business Review Vol. 10, Dec. 2021 pp. 25-42

Association of rhodamine cations with tetraphenylborate-anion in aqueous solution: structural properties of ions and stability of associates

The ability of rhodamine cations to form cation-anionic associates with tetraphenylborate-anion in an aqueous solution has been studied. The thermodynamic values of the equilibrium association constants Kasт were determined spectrophotometrically. The values of a number of properties of dye molecules (surface area, effective volume, hydrophobicity index log P, standard enthalpy of hydration ΔНohydr) were calculated using the QSAR model. The possibility of dependence of the value of Kasт on these factors has been reviewed. It was shown that changes in lg Kasт in the series of rhodamine associates are consistent with changes in the parameters log P and ΔНohydr.

Evaluation of microcolumn stability in ultrafast affinity extraction for binding and rate studies

Ultrafast affinity extraction (UAE) has recently been developed and employed for measuring non-bound (or free) fractions and binding or rate constants for drugs and other targets with soluble binding agents such as serum proteins. This study examined the long-term stability of 10 mm × 2.1 mm i.d. affinity microcolumns when used in UAE at both low and high flow rates (e.g., 0.5 and 3.5 mL/min) over an extended series of injections. This stability was investigated by using immobilized human serum albumin (HSA) and samples containing the drug warfarin with or without soluble HSA as a model system. The free warfarin fractions measured at 0.5 mL/min in the presence of soluble HSA were stable up to 150 injections and changed by <10% at 3.5 mL/min. The association equilibrium constant for warfarin with HSA that was estimated by UAE at 3.5 mL/min had no significant change over 50 injections and a change of only ∼18–22% over 100–150 injections. The dissociation rate constant for warfarin from HSA was found by combining UAE results at 0.5 and 3.5 mL/min and employing a new two-point approach, with no significant changes in this value being seen even after 200 injections. The effects of extended microcolumn use on the retention time, peak width, and peak asymmetry for warfarin, and on the backpressure of the microcolumn, were also considered. These results indicated that UAE and HSA microcolumns could be used to provide consistent values for free solute fractions, binding constants, and rate constants over a large series of injections. These results should be useful in future work by providing guidelines for the assessment, further development, and use of UAE in characterizing interactions involving other drugs and binding agents in solution-based samples.

Elucidation of specific binding sites and extraction of toxic Gen X from HSA employing cyclodextrin

The presence of per and poly-fluoroalkyl substances (PFAS), commonly referred to as forever chemicals, in aquatic systems is a serious global health problem. While the remediation of PFAS from aqueous media has been extensively investigated, their interactions with and removal from biological systems have received far less attention. We report herein structural alterations to human serum albumin (HSA) upon addition of perfluoro(2-methyl-3-oxahexanoic) acid (Gen X) monitored by changes to the fluorescence and circular dichroism (CD) spectra of HSA. The equilibrium association constant for Gen X binding to HSA is 7( ± 1) × 103 M−1 determined from changes in HSA fluorescence emission data during titration. Site-specific HSA binding fluorophores, 8-anilinonaphthalene-1-sulfonic acid (1,8-ANS), warfarin and dansyl-L-proline were used to investigate the specific binding sites of Gen X on HSA. A competitive displacement study yields association constants for Gen X to HSA at the 1,8-ANS, warfarin, and dansyl-L-proline binding sites to be 6.25 ( ± 0.5) × 104 M−1, 1.1 × 106 M−1, and 2.5( ± 0.2) × 109 M−1 respectively. Addition of β-cyclodextrin (β-CD) and heptakis(6-deoxy-6-amino)-β-cyclodextrin heptahydrochloride to the HSA:Gen X complex leads to the effective extraction of Gen X from the complex with the return of HSA in its native form. Gen X also leads to displacement of site-specific binding fluorophores bound to HSA, while subsequent addition of β-CD extracts Gen X from HSA with the return of the characteristic fluorescence of the HSA bound site-specific agent. These results illustrate the strong and specific binding sites of Gen X on HSA and demonstrate the principles for the potential application of β-CD for the remediation of PFAS from biological systems.

Heading towards sustainable environment: exploring the dynamic linkage among selected macroeconomic variables and ecological footprint using a novel dynamic ARDL simulations approach.

Ever since the emancipation of a country, its environmental quality has undergone a significant transition during the development phases; Bangladesh is no exception. Bangladesh is facing a serious threat in the age of global warming, and climate change as the country is looking forward in achieving the SDGs by 2030. Yet, there is a dearth of study regarding the relationship among crucial macroeconomic drivers and ecological footprint (a proxy for environmental degradation). Under the circumstances, this study explores the effects of economic growth, capital formation, urbanization, trade openness, energy use, and technological innovation on the ecological footprint by adopting the novel dynamic Autoregressive Distributed Lag (ARDL) simulations approach for Bangladesh, using annual frequency data from 1972 to 2017. Empirical results from the bounds test ascertained that there exists a long-run equilibrium association among the outlined variables. Furthermore, the novel dynamic ARDL simulation results revealed that Bangladesh is yet to achieve the environmental Kuznets curve (EKC) hypothesis. It was observed that the Bangladesh economy is still at the scale stage of its economic trajectory, emphasizing economic growth relative to her environmental status. However, capital formation, urbanization, and energy use seemed to degrade environmental quality, while trade openness and technological innovation upgraded the environmental quality. Putting it more elaborately, a unit escalation in GDP per capita increases the ecological footprint by 0.829% in the long run, while a unit increase in energy consumption upsurges the ecological footprint by 1.074% and 0.761% in the long run and short run, respectively. As regards technology innovation, one unit increase in it cutbacks the ecological footprint by 0.596% in the long run. Furthermore, the frequency domain causality unveiled the long-run feedback effect between economic growth and ecological footprint. The study further presents possible recommendations that can sustainably address environmental issues, keeping the economy buoyant.

The nexus amid foreign direct investment, urbanization, and CO2 emissions: Evidence from energy grouping along the ECOWAS community.

The vision of every country or subregions is to achieve economic growth and sustainable economic growth. Thus, the Economic Community of West African States (ECOWAS) as an economic cooperation renders interaction among 16 relevant countries to increase economic development. However, CO2 emissions as a result of economic growth are of great concern. Thus, this study delves into the determinants of CO2 emissions along the ECOWAS community, taking into consideration if countries are energy exporters or energy importers. The analytical procedure applied indicated the presence of heterogeneity in the slope coefficient and cross-sectional dependencies across the various panels. Applying the Westerlund bootstrap co-integration unveiled, the employed variables have a long-run equilibrium association. The results from the augmented mean group (AMG) revealed that the contribution weight (order of importance) to CO2 emissions varies across panel clusters. Finally, the causality results unveil a bidirectional causation in all panels between urbanization and CO2 emissions, whereas foreign direct investment and CO2 emissions have a bidirectional effect in energy importers and the main panel. These results obtained indicate that foreign direct investment, urbanization, energy consumption, trade openness, and gross domestic product are the determinants of CO2 emissions along the community. Based on the outcome, the suggested policy implications indicate that (a) the need for a paradigm shift from fossil fuel sources to renewables be encouraged in the community and (b) again, the awareness of spillover of economic growth and energy transition on CO2 emissions from foreign companies to local businesses must be promoted.

Cucurbituril-mediated AIE: An unconventional indicator displacement assay for ketamine detection

Typical AIE luminogens with extensive π-electron conjugation are limited in use on account of their complex synthesis, high cost and environmental concerns. To this end, we report here a novel host-guest inclusion complex that is assembled from nonemissive ligands, and surprisingly exhibits notable AIE features in aqueous solution while maintaining good sensitivity for ketamine (KET) detection. Isothermal titration studies confirm that palmatine (PAL) binds to cucurbit[8]uril (Q8) in a 2:1 ratio with an equilibrium association constant of 1.75 × 1011 M−2, suggesting that the unconventional AIE effects can be attributed to the stacking of two PAL moieties inside a single Q8 cavity. Geometric constraints of the macrocycle result in dimeric coupling of PAL in the ground state with significant bathochromic shifts in absorption and emission, which can be readily excited to exhibit enhanced photoluminescence. The unusual upfield perturbation and broadening of Q8 signals in the 1H NMR spectrum upon binding with PAL convey decisive information that Q8 not only serves as a molecular container, but also participates in the electron delocalization during the AIE events. Upon addition of KET, fluorescence was switched off through guest exchange to generate KET@Q8 as well as free PAL. The significant AIE characteristics of 2*PAL@Q8 in combination with its specific molecular recognition towards KET gives rise to 5.0 ng/mL limit of detection with linear range from 16.8 to 500 ng/mL, and a pronounced selectivity over possible interfering substances in biological matrices. We demonstrate the first example of Q8-mediated AIE effects, where the photoluminescence of virtually nonemissive or feebly emissive ligands is remarkably intensified through clustering inside a macrocyclic host molecule, therefore offering great promise for further development into dedicated AIE-based sensors.

Modeling the impact of climatic and non-climatic factors on cereal production: evidence from Indian agricultural sector.

The underpinned study examines the effects of climatic and non-climatic factors on Indian agriculture, cereal production, and yield using the country-level time series data of 1965-2015. With the autoregressive distributed lag (ARDL) bounds testing approach, the long-term equilibrium association among the variables has been explored. The results reveal that climatic factors like CO2 emissions and temperature adversely affect agricultural output, while rainfall positively affects it. Likewise, non-climatic factors, including energy used, financial development, and labor force, affect agricultural production positively in the long run. The estimated long-run results further demonstrate that CO2 emissions and rainfall positively affect both cereal production and yield, while temperature adversely affects them. The results exhibit that the cereal cropped area, energy used, financial development, and labor force significantly and positively impact the long-run cereal production and yield. Finally, pairwise Granger causality test confirmed that both climatic and non-climatic factors are significantly influencing agriculture and cereal production in India. Based on these results, policymakers and governmental institutions should formulate coherent adaptation measures and mitigation policies to tackle the adverse climate change effects on agriculture and its production of cereals.

The Kiselev isotherm for adsorption at the liquid-solid interface: Solving the mystery of negative equilibrium constants

Equilibrium data for aqueous adsorption systems are often correlated using isotherm models originally developed for adsorption at the gas-solid interface. A prominent example is the Langmuir isotherm, which has been used in thousands of investigations to describe the adsorption of dissolved substances at the liquid-solid interface. Another example is the Kiselev isotherm, which was proposed to account for adsorption at the gas-solid interface when adsorbate-adsorbate interactions are significant. Researchers who have applied the Kiselev isotherm to adsorption data for liquid-solid systems were puzzled by the fact that data fittings in most cases returned negative values for the adsorbate-adsorbate association equilibrium constant. It is shown in the present study that the data fitting problem is a direct consequence of misusing the Kiselev isotherm. In all previous studies, the Kiselev isotherm was used to fit type I isotherm data. Because the concept of adsorbate-adsorbate interactions is incompatible with a type I isotherm, fitting the Kiselev isotherm to such data can lead to nonsensical parameter estimates. The Kiselev isotherm was devised to account for type V isotherms exhibiting a sigmoid or S-shaped data trend. Physically meaningful parameter estimates can be obtained if the Kiselev isotherm is applied to type V isotherm data.